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SPC-Clean: A napari Plugin for Reducing Speckle and Isolated Pixel Noise in Fluorescence Microscopy Images

Alirezazadeh, P.; Kirsch, E. M.; Tian, Y.; Bewersdorf, J.; Rittscher, J.; Mergenthaler, P.

2026-08-27 bioinformatics
10.64898/2026.08.24.744862 bioRxiv
Show abstract

Speckle artifacts and isolated foreground pixels are common in fluorescence microscopy and can interfere with segmentation and subsequent quantitative image analysis. Conventional denoising methods often modify image intensities through filtering or smoothing, potentially altering biologically relevant fluorescence signals. We introduce Sparse Pixel Cluster Cleaning (SPC-Clean), a topology-aware method that removes poorly supported foreground pixels through iterative neighborhood analysis of a thresholded mask. SPC-Clean is deterministic, training-free, preserves original fluorescence intensities for practical microscopy workflows.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.